Starting phenix.real_space_refine on Thu Aug 6 08:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jsl_36622/08_2026/8jsl_36622.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 S 76 5.16 5 C 8953 2.51 5 N 2385 2.21 5 O 2644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14069 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 10897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1362, 10897 Classifications: {'peptide': 1362} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 70, 'TRANS': 1289} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1799 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 235, 1793 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 217} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 235, 1793 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 217} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1823 Chain: "C" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 533 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 303 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 324 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNAv2': 10} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 4} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9157 SG CYS A1150 47.347 43.269 98.527 1.00 95.98 S ATOM 9179 SG CYS A1153 50.110 40.569 98.102 1.00 97.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 266 " occ=0.67 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.33 Time building chain proxies: 3.34, per 1000 atoms: 0.24 Number of scatterers: 14069 At special positions: 0 Unit cell: (144.42, 133.63, 114.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 76 16.00 P 10 15.00 O 2644 8.00 N 2385 7.00 C 8953 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 706.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " Number of angles added : 2 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 56.8% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.613A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.676A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 72 through 75 removed outlier: 3.727A pdb=" N PHE A 75 " --> pdb=" O PRO A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 100 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.510A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.534A pdb=" N MET A 210 " --> pdb=" O HIS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.023A pdb=" N LYS A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 261 removed outlier: 3.549A pdb=" N ILE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.503A pdb=" N ILE A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 Processing helix chain 'A' and resid 438 through 446 removed outlier: 4.390A pdb=" N TYR A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 Processing helix chain 'A' and resid 477 through 482 removed outlier: 3.864A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 482 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 498 removed outlier: 3.530A pdb=" N TRP A 494 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASP A 495 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL A 497 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 498 " --> pdb=" O ASP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.599A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.582A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 610 Processing helix chain 'A' and resid 634 through 640 removed outlier: 4.156A pdb=" N ASN A 637 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.655A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 688 through 692 removed outlier: 4.071A pdb=" N ARG A 691 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASN A 692 " --> pdb=" O GLU A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 692' Processing helix chain 'A' and resid 712 through 731 removed outlier: 3.527A pdb=" N TRP A 716 " --> pdb=" O GLN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 4.232A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS A 783 " --> pdb=" O VAL A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.877A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.728A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 889 removed outlier: 3.732A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 889' Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 927 through 943 Processing helix chain 'A' and resid 948 through 955 removed outlier: 4.277A pdb=" N LYS A 955 " --> pdb=" O PRO A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 974 through 978 removed outlier: 3.648A pdb=" N GLN A 978 " --> pdb=" O PRO A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 Processing helix chain 'A' and resid 1000 through 1005 Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.827A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 removed outlier: 3.509A pdb=" N GLY A1048 " --> pdb=" O LEU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.530A pdb=" N LEU A1056 " --> pdb=" O GLY A1052 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1064 Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.578A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1134 through 1137 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1182 through 1184 No H-bonds generated for 'chain 'A' and resid 1182 through 1184' Processing helix chain 'A' and resid 1213 through 1230 Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 4.062A pdb=" N ILE A1240 " --> pdb=" O SER A1236 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1254 through 1259 removed outlier: 3.912A pdb=" N MET A1258 " --> pdb=" O GLU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.551A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 Processing helix chain 'A' and resid 1335 through 1339 Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 149 removed outlier: 4.025A pdb=" N THR B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 removed outlier: 3.683A pdb=" N ALA B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 232 removed outlier: 3.544A pdb=" N HIS B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.835A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.546A pdb=" N GLY B 270 " --> pdb=" O ASER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 304 through 309 removed outlier: 4.342A pdb=" N LYS B 309 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 119 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.589A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'D' and resid 111 through 116 removed outlier: 3.603A pdb=" N GLU D 115 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 146 removed outlier: 3.600A pdb=" N TYR D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP D 123 " --> pdb=" O LYS D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 117 Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.813A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.859A pdb=" N SER B 174 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.837A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'A' and resid 1175 through 1176 removed outlier: 3.805A pdb=" N SER A1175 " --> pdb=" O ILE A1187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296 659 hydrogen bonds defined for protein. 1852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4310 1.34 - 1.45: 2098 1.45 - 1.57: 7877 1.57 - 1.69: 19 1.69 - 1.81: 111 Bond restraints: 14415 Sorted by residual: bond pdb=" N TYR A1088 " pdb=" CA TYR A1088 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.42e+00 bond pdb=" N LEU A1089 " pdb=" CA LEU A1089 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.54e-02 4.22e+03 5.18e+00 bond pdb=" N ASP A1090 " pdb=" CA ASP A1090 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.96e+00 bond pdb=" N GLU C 178 " pdb=" CA GLU C 178 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.95e+00 bond pdb=" CA TYR A1088 " pdb=" C TYR A1088 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 2.92e+00 ... (remaining 14410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 19258 1.88 - 3.76: 317 3.76 - 5.65: 44 5.65 - 7.53: 10 7.53 - 9.41: 2 Bond angle restraints: 19631 Sorted by residual: angle pdb=" N TYR A 51 " pdb=" CA TYR A 51 " pdb=" C TYR A 51 " ideal model delta sigma weight residual 114.56 107.58 6.98 1.27e+00 6.20e-01 3.02e+01 angle pdb=" CA LEU A1089 " pdb=" C LEU A1089 " pdb=" O LEU A1089 " ideal model delta sigma weight residual 122.03 118.02 4.01 1.17e+00 7.31e-01 1.17e+01 angle pdb=" C SER A 750 " pdb=" N VAL A 751 " pdb=" CA VAL A 751 " ideal model delta sigma weight residual 121.97 127.82 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C GLU B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.30e+00 angle pdb=" CA TYR A 51 " pdb=" C TYR A 51 " pdb=" N ARG A 52 " ideal model delta sigma weight residual 119.26 115.86 3.40 1.14e+00 7.69e-01 8.88e+00 ... (remaining 19626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7802 17.90 - 35.80: 700 35.80 - 53.70: 114 53.70 - 71.60: 42 71.60 - 89.50: 14 Dihedral angle restraints: 8672 sinusoidal: 3524 harmonic: 5148 Sorted by residual: dihedral pdb=" C4' U G 0 " pdb=" C3' U G 0 " pdb=" C2' U G 0 " pdb=" C1' U G 0 " ideal model delta sinusoidal sigma weight residual 36.35 -36.12 72.47 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' G G 3 " pdb=" C3' G G 3 " pdb=" C2' G G 3 " pdb=" C1' G G 3 " ideal model delta sinusoidal sigma weight residual 36.34 -36.11 72.45 1 3.10e+00 1.04e-01 6.98e+02 dihedral pdb=" C4' U G 2 " pdb=" C3' U G 2 " pdb=" C2' U G 2 " pdb=" C1' U G 2 " ideal model delta sinusoidal sigma weight residual 36.34 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 ... (remaining 8669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1916 0.057 - 0.114: 282 0.114 - 0.171: 17 0.171 - 0.228: 5 0.228 - 0.285: 16 Chirality restraints: 2236 Sorted by residual: chirality pdb=" C2' C G 7 " pdb=" C3' C G 7 " pdb=" O2' C G 7 " pdb=" C1' C G 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' G G 3 " pdb=" C3' G G 3 " pdb=" O2' G G 3 " pdb=" C1' G G 3 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' U G 2 " pdb=" C3' U G 2 " pdb=" O2' U G 2 " pdb=" C1' U G 2 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2233 not shown) Planarity restraints: 2476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1085 " 0.011 2.00e-02 2.50e+03 1.34e-02 4.47e+00 pdb=" CG TRP A1085 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A1085 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A1085 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1085 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A1085 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1085 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1085 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1085 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1145 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A1146 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A1146 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1146 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 550 " 0.012 2.00e-02 2.50e+03 1.09e-02 2.08e+00 pdb=" CG PHE A 550 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 550 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 550 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 550 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 550 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 550 " 0.002 2.00e-02 2.50e+03 ... (remaining 2473 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1248 2.74 - 3.28: 13515 3.28 - 3.82: 21991 3.82 - 4.36: 25536 4.36 - 4.90: 46230 Nonbonded interactions: 108520 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OH TYR A 922 " model vdw 2.203 3.040 nonbonded pdb=" ND2 ASN A1249 " pdb=" OH TYR A1381 " model vdw 2.255 3.120 nonbonded pdb=" O ARG D 110 " pdb=" OG SER D 113 " model vdw 2.259 3.040 nonbonded pdb=" O CYS B 275 " pdb=" NE2 GLN B 279 " model vdw 2.266 3.120 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.270 3.040 ... (remaining 108515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 110 through 118 or (resid 119 and (name N or name CA or na \ me C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 110 through 132 or (resid 133 and (name N or name CA or na \ me C or name O or name CB )) or resid 134 through 146)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14419 Z= 0.125 Angle : 0.594 20.030 19633 Z= 0.298 Chirality : 0.046 0.285 2236 Planarity : 0.004 0.037 2476 Dihedral : 14.614 89.497 5336 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.17 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.21), residues: 1738 helix: 1.99 (0.19), residues: 850 sheet: 1.43 (0.60), residues: 81 loop : -1.27 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 433 TYR 0.019 0.001 TYR A 636 PHE 0.025 0.001 PHE A 550 TRP 0.035 0.001 TRP A1085 HIS 0.005 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (14415) covalent geometry : angle 0.57693 / 0.30 (19631) hydrogen bonds : bond 0.16684 / 11.22 ( 659) hydrogen bonds : angle 4.53574 / 3.14 ( 1852) metal coordination : bond 0.00494 / 0.25 ( 4) metal coordination : angle 14.18950 / 7.47 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.7731 (m-30) cc_final: 0.7455 (m-30) REVERT: A 238 ILE cc_start: 0.8657 (mm) cc_final: 0.8194 (mm) REVERT: A 242 ASP cc_start: 0.8049 (m-30) cc_final: 0.7818 (m-30) REVERT: A 990 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7485 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7785 (m-40) cc_final: 0.7401 (p0) REVERT: A 1340 GLN cc_start: 0.7924 (pm20) cc_final: 0.7617 (pm20) REVERT: B 165 GLU cc_start: 0.8024 (pm20) cc_final: 0.7777 (pm20) outliers start: 0 outliers final: 1 residues processed: 233 average time/residue: 0.6641 time to fit residues: 168.6469 Evaluate side-chains 175 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.3980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A 743 ASN A 978 GLN A1120 HIS A1253 GLN ** A1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1333 ASN A1342 ASN B 279 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.135028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.092595 restraints weight = 34093.110| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.69 r_work: 0.2761 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14419 Z= 0.195 Angle : 0.733 16.646 19633 Z= 0.348 Chirality : 0.059 1.015 2236 Planarity : 0.005 0.040 2476 Dihedral : 7.976 133.208 2013 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.74 % Favored : 92.85 % Rotamer: Outliers : 1.56 % Allowed : 9.39 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1738 helix: 1.87 (0.19), residues: 860 sheet: 1.46 (0.59), residues: 86 loop : -1.31 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 491 TYR 0.018 0.002 TYR A 427 PHE 0.026 0.002 PHE A 550 TRP 0.018 0.001 TRP A1085 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (14415) covalent geometry : angle 0.73071 / 0.35 (19631) hydrogen bonds : bond 0.06107 / 4.14 ( 659) hydrogen bonds : angle 3.90187 / 2.73 ( 1852) metal coordination : bond 0.01113 / 0.56 ( 4) metal coordination : angle 6.21857 / 3.30 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.540 Fit side-chains REVERT: A 154 ASP cc_start: 0.8609 (m-30) cc_final: 0.8358 (m-30) REVERT: A 203 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.7642 (mp10) REVERT: A 242 ASP cc_start: 0.8830 (m-30) cc_final: 0.8611 (m-30) REVERT: A 518 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 578 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: A 814 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: A 990 ARG cc_start: 0.8463 (tpt170) cc_final: 0.8072 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7792 (m-30) cc_final: 0.7262 (m-30) REVERT: A 1064 ASN cc_start: 0.7579 (m-40) cc_final: 0.7113 (p0) REVERT: A 1340 GLN cc_start: 0.8242 (pm20) cc_final: 0.7604 (pm20) REVERT: B 165 GLU cc_start: 0.8120 (pm20) cc_final: 0.7841 (pm20) REVERT: E 132 ASN cc_start: 0.8684 (t160) cc_final: 0.8459 (t0) outliers start: 24 outliers final: 13 residues processed: 210 average time/residue: 0.6846 time to fit residues: 156.2277 Evaluate side-chains 200 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 814 GLN Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 137 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A1120 HIS A1266 ASN A1269 HIS A1342 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.093409 restraints weight = 35307.336| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.84 r_work: 0.2776 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14419 Z= 0.141 Angle : 0.628 11.309 19633 Z= 0.309 Chirality : 0.049 0.683 2236 Planarity : 0.004 0.038 2476 Dihedral : 8.117 147.150 2013 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.22 % Favored : 93.43 % Rotamer: Outliers : 1.76 % Allowed : 12.26 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.21), residues: 1738 helix: 1.93 (0.19), residues: 865 sheet: 1.34 (0.57), residues: 86 loop : -1.33 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.016 0.001 TYR A 427 PHE 0.017 0.001 PHE A 550 TRP 0.010 0.001 TRP A1085 HIS 0.004 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (14415) covalent geometry : angle 0.62576 / 0.31 (19631) hydrogen bonds : bond 0.05105 / 3.46 ( 659) hydrogen bonds : angle 3.78592 / 2.64 ( 1852) metal coordination : bond 0.01024 / 0.51 ( 4) metal coordination : angle 5.45262 / 2.87 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.563 Fit side-chains REVERT: A 154 ASP cc_start: 0.8606 (m-30) cc_final: 0.8352 (m-30) REVERT: A 203 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: A 242 ASP cc_start: 0.8826 (m-30) cc_final: 0.8602 (m-30) REVERT: A 556 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8318 (mt-10) REVERT: A 578 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: A 990 ARG cc_start: 0.8481 (tpt170) cc_final: 0.8059 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7793 (m-30) cc_final: 0.7205 (m-30) REVERT: A 1064 ASN cc_start: 0.7578 (m-40) cc_final: 0.7088 (p0) REVERT: A 1245 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7670 (tm-30) REVERT: A 1338 ASP cc_start: 0.8330 (t0) cc_final: 0.8127 (t0) REVERT: A 1340 GLN cc_start: 0.8191 (pm20) cc_final: 0.7657 (pm20) REVERT: A 1381 TYR cc_start: 0.8078 (t80) cc_final: 0.7873 (t80) REVERT: B 165 GLU cc_start: 0.8129 (pm20) cc_final: 0.7893 (pm20) REVERT: B 339 LYS cc_start: 0.6932 (tppt) cc_final: 0.6408 (tppt) REVERT: D 141 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8312 (mmtt) outliers start: 27 outliers final: 11 residues processed: 207 average time/residue: 0.6839 time to fit residues: 153.9922 Evaluate side-chains 191 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 9 optimal weight: 0.0470 chunk 132 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 147 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 chunk 83 optimal weight: 0.9980 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A 608 GLN A 743 ASN A1120 HIS A1266 ASN A1342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100165 restraints weight = 27378.797| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.08 r_work: 0.2857 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14419 Z= 0.103 Angle : 0.559 11.264 19633 Z= 0.274 Chirality : 0.042 0.331 2236 Planarity : 0.004 0.037 2476 Dihedral : 7.616 141.743 2011 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.94 % Favored : 93.72 % Rotamer: Outliers : 1.63 % Allowed : 13.49 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1738 helix: 2.08 (0.19), residues: 864 sheet: 1.17 (0.57), residues: 86 loop : -1.23 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.010 0.001 TYR B 142 PHE 0.014 0.001 PHE A 270 TRP 0.009 0.001 TRP A1085 HIS 0.008 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (14415) covalent geometry : angle 0.55779 / 0.27 (19631) hydrogen bonds : bond 0.03479 / 2.34 ( 659) hydrogen bonds : angle 3.58988 / 2.50 ( 1852) metal coordination : bond 0.00773 / 0.39 ( 4) metal coordination : angle 3.25577 / 1.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8552 (m-30) cc_final: 0.8256 (m-30) REVERT: A 238 ILE cc_start: 0.8560 (mm) cc_final: 0.8092 (mm) REVERT: A 242 ASP cc_start: 0.8750 (m-30) cc_final: 0.8515 (m-30) REVERT: A 518 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: A 578 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7543 (tp30) REVERT: A 628 SER cc_start: 0.9038 (p) cc_final: 0.8797 (t) REVERT: A 990 ARG cc_start: 0.8383 (tpt170) cc_final: 0.7965 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7456 (m-40) cc_final: 0.6915 (p0) REVERT: A 1245 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7896 (tm-30) REVERT: A 1338 ASP cc_start: 0.8346 (t0) cc_final: 0.7982 (t0) REVERT: A 1340 GLN cc_start: 0.8222 (pm20) cc_final: 0.7676 (pm20) REVERT: A 1381 TYR cc_start: 0.8044 (t80) cc_final: 0.7809 (t80) outliers start: 25 outliers final: 4 residues processed: 213 average time/residue: 0.5786 time to fit residues: 135.2673 Evaluate side-chains 196 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 190 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 518 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 18 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A1120 HIS A1266 ASN A1269 HIS A1342 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096222 restraints weight = 36083.976| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.01 r_work: 0.2812 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14419 Z= 0.116 Angle : 0.570 8.176 19633 Z= 0.281 Chirality : 0.043 0.334 2236 Planarity : 0.004 0.045 2476 Dihedral : 7.566 142.272 2011 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.71 % Favored : 93.95 % Rotamer: Outliers : 2.02 % Allowed : 14.21 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.21), residues: 1738 helix: 2.10 (0.19), residues: 865 sheet: 1.25 (0.58), residues: 86 loop : -1.20 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 312 TYR 0.011 0.001 TYR A 427 PHE 0.015 0.001 PHE A 548 TRP 0.007 0.001 TRP A 191 HIS 0.007 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14415) covalent geometry : angle 0.56853 / 0.28 (19631) hydrogen bonds : bond 0.03977 / 2.69 ( 659) hydrogen bonds : angle 3.56212 / 2.48 ( 1852) metal coordination : bond 0.00859 / 0.43 ( 4) metal coordination : angle 4.04900 / 2.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8589 (m-30) cc_final: 0.8292 (m-30) REVERT: A 203 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: A 242 ASP cc_start: 0.8795 (m-30) cc_final: 0.8552 (m-30) REVERT: A 578 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: A 628 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8849 (t) REVERT: A 990 ARG cc_start: 0.8468 (tpt170) cc_final: 0.8040 (tpm-80) REVERT: A 1064 ASN cc_start: 0.7512 (m-40) cc_final: 0.6966 (p0) REVERT: A 1245 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7996 (tm-30) REVERT: A 1338 ASP cc_start: 0.8410 (t0) cc_final: 0.8019 (t0) REVERT: A 1340 GLN cc_start: 0.8260 (pm20) cc_final: 0.7728 (pm20) REVERT: A 1381 TYR cc_start: 0.8075 (t80) cc_final: 0.7857 (t80) REVERT: B 165 GLU cc_start: 0.8071 (pm20) cc_final: 0.7842 (pm20) REVERT: E 137 GLU cc_start: 0.8106 (tp30) cc_final: 0.7879 (tp30) outliers start: 31 outliers final: 13 residues processed: 211 average time/residue: 0.6693 time to fit residues: 154.0709 Evaluate side-chains 190 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 87 optimal weight: 0.0030 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 0.0170 chunk 71 optimal weight: 0.5980 overall best weight: 0.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A 168 ASN A 743 ASN A1120 HIS A1266 ASN A1269 HIS A1342 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100493 restraints weight = 29247.974| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.16 r_work: 0.2863 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14419 Z= 0.105 Angle : 0.559 10.013 19633 Z= 0.274 Chirality : 0.042 0.321 2236 Planarity : 0.004 0.044 2476 Dihedral : 7.487 141.937 2011 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.76 % Favored : 93.89 % Rotamer: Outliers : 1.96 % Allowed : 14.60 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1738 helix: 2.18 (0.19), residues: 863 sheet: 1.19 (0.58), residues: 88 loop : -1.22 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 312 TYR 0.010 0.001 TYR B 142 PHE 0.012 0.001 PHE A 548 TRP 0.007 0.001 TRP A 173 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (14415) covalent geometry : angle 0.55779 / 0.27 (19631) hydrogen bonds : bond 0.03569 / 2.41 ( 659) hydrogen bonds : angle 3.49028 / 2.41 ( 1852) metal coordination : bond 0.00779 / 0.39 ( 4) metal coordination : angle 3.48625 / 1.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8538 (m-30) cc_final: 0.8231 (m-30) REVERT: A 197 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (pt) REVERT: A 203 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: A 242 ASP cc_start: 0.8704 (m-30) cc_final: 0.8454 (m-30) REVERT: A 578 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7564 (tp30) REVERT: A 628 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8826 (t) REVERT: A 990 ARG cc_start: 0.8462 (tpt170) cc_final: 0.8038 (tpm-80) REVERT: A 1033 ASP cc_start: 0.8550 (t70) cc_final: 0.8241 (t0) REVERT: A 1064 ASN cc_start: 0.7487 (m-40) cc_final: 0.6946 (p0) REVERT: A 1245 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7925 (tm-30) REVERT: A 1338 ASP cc_start: 0.8362 (t0) cc_final: 0.7967 (t0) REVERT: A 1340 GLN cc_start: 0.8201 (pm20) cc_final: 0.7705 (pm20) REVERT: A 1381 TYR cc_start: 0.8044 (t80) cc_final: 0.7813 (t80) REVERT: B 165 GLU cc_start: 0.8018 (pm20) cc_final: 0.7814 (pm20) REVERT: B 339 LYS cc_start: 0.6904 (tppt) cc_final: 0.6229 (tppt) outliers start: 30 outliers final: 12 residues processed: 209 average time/residue: 0.6538 time to fit residues: 149.2507 Evaluate side-chains 194 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain C residue 141 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 83 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 50 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 111 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A1120 HIS A1266 ASN A1269 HIS A1342 ASN B 166 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.140074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100561 restraints weight = 23932.402| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.66 r_work: 0.2889 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14419 Z= 0.106 Angle : 0.573 11.340 19633 Z= 0.277 Chirality : 0.041 0.319 2236 Planarity : 0.004 0.056 2476 Dihedral : 7.446 141.847 2011 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.42 % Favored : 94.24 % Rotamer: Outliers : 2.15 % Allowed : 14.86 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1738 helix: 2.21 (0.19), residues: 863 sheet: 1.22 (0.57), residues: 90 loop : -1.21 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 312 TYR 0.010 0.001 TYR B 142 PHE 0.013 0.001 PHE A 548 TRP 0.007 0.001 TRP A 191 HIS 0.005 0.001 HIS A1269 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (14415) covalent geometry : angle 0.57217 / 0.28 (19631) hydrogen bonds : bond 0.03554 / 2.40 ( 659) hydrogen bonds : angle 3.47136 / 2.40 ( 1852) metal coordination : bond 0.00747 / 0.37 ( 4) metal coordination : angle 3.48027 / 1.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ASP cc_start: 0.8487 (m-30) cc_final: 0.8177 (m-30) REVERT: A 197 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8303 (pt) REVERT: A 203 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: A 242 ASP cc_start: 0.8649 (m-30) cc_final: 0.8394 (m-30) REVERT: A 578 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7509 (tp30) REVERT: A 628 SER cc_start: 0.9031 (OUTLIER) cc_final: 0.8792 (t) REVERT: A 711 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7432 (mt) REVERT: A 990 ARG cc_start: 0.8424 (tpt170) cc_final: 0.7995 (tpm-80) REVERT: A 1033 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8199 (t0) REVERT: A 1064 ASN cc_start: 0.7466 (m-40) cc_final: 0.6937 (p0) REVERT: A 1338 ASP cc_start: 0.8356 (t0) cc_final: 0.7946 (t0) REVERT: A 1340 GLN cc_start: 0.8198 (pm20) cc_final: 0.7696 (pm20) REVERT: A 1381 TYR cc_start: 0.8036 (t80) cc_final: 0.7830 (t80) REVERT: B 312 ARG cc_start: 0.6861 (ttm110) cc_final: 0.6334 (ttm-80) REVERT: C 124 MET cc_start: 0.6501 (mmp) cc_final: 0.6243 (mmp) outliers start: 33 outliers final: 15 residues processed: 205 average time/residue: 0.5884 time to fit residues: 132.5132 Evaluate side-chains 208 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 117 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.0970 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A 743 ASN A1120 HIS A1266 ASN A1269 HIS ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095258 restraints weight = 31352.448| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.41 r_work: 0.2751 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14419 Z= 0.175 Angle : 0.638 11.154 19633 Z= 0.314 Chirality : 0.045 0.356 2236 Planarity : 0.004 0.038 2476 Dihedral : 7.633 141.117 2011 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.05 % Favored : 93.43 % Rotamer: Outliers : 2.02 % Allowed : 15.25 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1738 helix: 2.08 (0.19), residues: 859 sheet: 1.26 (0.59), residues: 88 loop : -1.25 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 312 TYR 0.019 0.002 TYR A 427 PHE 0.022 0.002 PHE A 548 TRP 0.008 0.001 TRP A 664 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.17 (14415) covalent geometry : angle 0.63615 / 0.31 (19631) hydrogen bonds : bond 0.05378 / 3.63 ( 659) hydrogen bonds : angle 3.63216 / 2.52 ( 1852) metal coordination : bond 0.01024 / 0.52 ( 4) metal coordination : angle 5.41292 / 2.86 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.524 Fit side-chains REVERT: A 154 ASP cc_start: 0.8633 (m-30) cc_final: 0.8350 (m-30) REVERT: A 197 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8546 (pt) REVERT: A 203 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: A 242 ASP cc_start: 0.8821 (m-30) cc_final: 0.8577 (m-30) REVERT: A 578 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: A 711 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7461 (mt) REVERT: A 990 ARG cc_start: 0.8515 (tpt170) cc_final: 0.8059 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7811 (m-30) cc_final: 0.7234 (m-30) REVERT: A 1033 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8209 (t0) REVERT: A 1064 ASN cc_start: 0.7575 (m-40) cc_final: 0.7043 (p0) REVERT: A 1338 ASP cc_start: 0.8407 (t0) cc_final: 0.7981 (t0) REVERT: A 1340 GLN cc_start: 0.8278 (pm20) cc_final: 0.7809 (pm20) REVERT: A 1381 TYR cc_start: 0.8182 (t80) cc_final: 0.7850 (t80) REVERT: B 165 GLU cc_start: 0.8065 (pm20) cc_final: 0.7806 (pm20) REVERT: B 339 LYS cc_start: 0.7049 (tppt) cc_final: 0.6140 (tppt) outliers start: 31 outliers final: 16 residues processed: 206 average time/residue: 0.6416 time to fit residues: 143.9537 Evaluate side-chains 200 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 149 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A1120 HIS A1266 ASN A1269 HIS A1342 ASN ** B 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.136907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.094711 restraints weight = 36249.058| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.85 r_work: 0.2790 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14419 Z= 0.128 Angle : 0.616 11.467 19633 Z= 0.303 Chirality : 0.043 0.336 2236 Planarity : 0.004 0.038 2476 Dihedral : 7.589 141.549 2011 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.82 % Favored : 93.66 % Rotamer: Outliers : 1.96 % Allowed : 15.78 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1738 helix: 2.16 (0.19), residues: 859 sheet: 1.18 (0.58), residues: 88 loop : -1.25 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.013 0.001 TYR A 568 PHE 0.018 0.001 PHE A 548 TRP 0.007 0.001 TRP A 191 HIS 0.005 0.001 HIS B 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (14415) covalent geometry : angle 0.61405 / 0.30 (19631) hydrogen bonds : bond 0.04526 / 3.05 ( 659) hydrogen bonds : angle 3.58800 / 2.48 ( 1852) metal coordination : bond 0.00892 / 0.45 ( 4) metal coordination : angle 4.52096 / 2.38 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.567 Fit side-chains REVERT: A 154 ASP cc_start: 0.8611 (m-30) cc_final: 0.8349 (m-30) REVERT: A 197 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8502 (pt) REVERT: A 203 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: A 242 ASP cc_start: 0.8791 (m-30) cc_final: 0.8561 (m-30) REVERT: A 578 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: A 711 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7487 (mt) REVERT: A 990 ARG cc_start: 0.8509 (tpt170) cc_final: 0.8088 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7809 (m-30) cc_final: 0.7263 (m-30) REVERT: A 1033 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8270 (t0) REVERT: A 1064 ASN cc_start: 0.7569 (m-40) cc_final: 0.7052 (p0) REVERT: A 1338 ASP cc_start: 0.8388 (t0) cc_final: 0.7998 (t0) REVERT: A 1340 GLN cc_start: 0.8273 (pm20) cc_final: 0.7815 (pm20) REVERT: A 1381 TYR cc_start: 0.8082 (t80) cc_final: 0.7852 (t80) REVERT: B 339 LYS cc_start: 0.6969 (tppt) cc_final: 0.6287 (tppt) REVERT: C 124 MET cc_start: 0.6603 (mmp) cc_final: 0.6386 (mmp) outliers start: 30 outliers final: 19 residues processed: 200 average time/residue: 0.5890 time to fit residues: 129.0361 Evaluate side-chains 208 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1252 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 139 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A 743 ASN A1091 HIS A1120 HIS A1266 ASN A1269 HIS B 166 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093895 restraints weight = 29433.182| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.25 r_work: 0.2726 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14419 Z= 0.173 Angle : 0.664 11.572 19633 Z= 0.327 Chirality : 0.046 0.358 2236 Planarity : 0.004 0.063 2476 Dihedral : 7.691 141.315 2011 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.05 % Favored : 93.43 % Rotamer: Outliers : 1.89 % Allowed : 15.97 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1738 helix: 2.10 (0.19), residues: 846 sheet: 1.13 (0.58), residues: 88 loop : -1.23 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 312 TYR 0.019 0.002 TYR A 427 PHE 0.023 0.002 PHE A 548 TRP 0.008 0.001 TRP A 664 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 (14415) covalent geometry : angle 0.66192 / 0.33 (19631) hydrogen bonds : bond 0.05540 / 3.74 ( 659) hydrogen bonds : angle 3.69282 / 2.57 ( 1852) metal coordination : bond 0.01008 / 0.51 ( 4) metal coordination : angle 5.23270 / 2.76 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.527 Fit side-chains REVERT: A 154 ASP cc_start: 0.8664 (m-30) cc_final: 0.8408 (m-30) REVERT: A 197 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8590 (pt) REVERT: A 203 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: A 242 ASP cc_start: 0.8847 (m-30) cc_final: 0.8598 (m-30) REVERT: A 578 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: A 711 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7494 (mt) REVERT: A 990 ARG cc_start: 0.8504 (tpt170) cc_final: 0.8050 (tpm-80) REVERT: A 1013 ASP cc_start: 0.7833 (m-30) cc_final: 0.7270 (m-30) REVERT: A 1064 ASN cc_start: 0.7579 (m-40) cc_final: 0.7075 (p0) REVERT: A 1338 ASP cc_start: 0.8445 (t0) cc_final: 0.8032 (t0) REVERT: A 1340 GLN cc_start: 0.8286 (pm20) cc_final: 0.7789 (pm20) REVERT: A 1375 ARG cc_start: 0.6423 (mpt-90) cc_final: 0.5998 (mmt90) REVERT: A 1381 TYR cc_start: 0.8209 (t80) cc_final: 0.8001 (t80) REVERT: B 165 GLU cc_start: 0.8071 (pm20) cc_final: 0.7824 (pm20) REVERT: B 339 LYS cc_start: 0.7086 (tppt) cc_final: 0.6220 (tppt) REVERT: C 124 MET cc_start: 0.6525 (mmp) cc_final: 0.6288 (mmp) REVERT: D 124 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6736 (ttt) outliers start: 29 outliers final: 20 residues processed: 210 average time/residue: 0.6623 time to fit residues: 151.9654 Evaluate side-chains 203 residues out of total 1548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 637 ASN Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1334 THR Chi-restraints excluded: chain A residue 1351 CYS Chi-restraints excluded: chain A residue 1364 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 153 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 HIS A 97 GLN A1120 HIS A1266 ASN A1269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095824 restraints weight = 22450.089| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.55 r_work: 0.2803 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14419 Z= 0.131 Angle : 0.633 11.735 19633 Z= 0.312 Chirality : 0.043 0.336 2236 Planarity : 0.004 0.037 2476 Dihedral : 7.612 141.508 2011 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.82 % Favored : 93.66 % Rotamer: Outliers : 1.69 % Allowed : 16.43 % Favored : 81.88 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1738 helix: 2.19 (0.19), residues: 841 sheet: 1.05 (0.58), residues: 88 loop : -1.19 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 312 TYR 0.013 0.001 TYR A 427 PHE 0.019 0.001 PHE A 548 TRP 0.007 0.001 TRP A 173 HIS 0.006 0.001 HIS A 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (14415) covalent geometry : angle 0.63107 / 0.31 (19631) hydrogen bonds : bond 0.04616 / 3.11 ( 659) hydrogen bonds : angle 3.63350 / 2.52 ( 1852) metal coordination : bond 0.00920 / 0.46 ( 4) metal coordination : angle 4.48002 / 2.36 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5158.71 seconds wall clock time: 88 minutes 39.73 seconds (5319.73 seconds total)